IF your new receiver fits in the middle shelf, I'd put it there and put the center channel on the top shelf. The more you can have it "out in the open", the better. Set the speaker a little bit proud of the front lip of the top shelf, so that little (or none) of the shelf interacts with the speaker baffle.
If your new receiver only fits on the bottom shelf, I'd still do that and try really hard to put the speaker on the top shelf rather than in the middle.
But, yeah, PITA all the way around. Try to have fun.
